#'head: cannot open 'reference.fasta' for reading: No such file or directory' while running denovo assembly

[santoshkumarrana]

I was running denovo assembly on SE RAD-seq reads, and prepared all infile and config.ctl file according to dDocent manual. The program runs with an error somewhere in bwa saying: 'head: cannot open 'reference.fasta' for reading: No such file or directory' Creating alignment intervals Cannot open "reference.fasta.fai"No such file or directory mawk: cannot open reference.fasta.fai (No such file or directory) Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting.

I tried all the way re-installing conda env, packages, file permission (but file permission gets changed after running ddocent from '-rwxrwxrwx' to '-rw-rw----'. Please find the attached log file contents.

dDocent version 2.9.4 started Fri Feb 17 01:46:58 EST 2023

At this point, all configuration information has been entered and dDocent may take several hours to run. It is recommended that you move this script to a background operation and disable terminal input and output. All data and logfiles will still be recorded. To do this: Press control and Z simultaneously Type bg and press enter Type disown -h and press enter Now sit back, relax, and wait for your analysis to finish

Trimming reads Removing the _1 character and replacing with /1 in the name of every sequence

Using BWA to map reads head: cannot open 'reference.fasta' for reading: No such file or directory

Creating alignment intervals Cannot open "reference.fasta.fai"No such file or directory mawk: cannot open reference.fasta.fai (No such file or directory) Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. . . . Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting. Error: The genome file genome.file has no valid entries (are you sure it's a 2-column bedtools genome file). Exiting.

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***** ERROR: Requested column 4, but database file - only has fields 1 - 0. head: cannot open 'reference.fasta' for reading: No such file or directory

gzip: stdout: Broken pipe . . . gzip: stdout: Broken pipe

gzip: stdout: Broken pipe

gzip: stdout: Broken pipe Genomic interval creation completed successfully.

Using FreeBayes to call SNPs popmap file not found, building a new one from the sample names ls: cannot access 'mapped..bed': No such file or directory rm: cannot remove 'mapped..bed': No such file or directory could not open "raw..vcf" exiting mv: cannot stat 'raw..vcf': No such file or directory

Using VCFtools to parse TotalRawSNPS.vcf for SNPs that are called in at least 90% of individuals

dDocent has finished with an analysis in /storage/home/sqr5923/scratch/rudhir/ddocent

dDocent started Fri Feb 17 01:46:58 EST 2023

dDocent finished Fri Feb 17 04:08:54 EST 2023

After filtering, kept 0 out of a possible 0 Sites

dDocent 2.9.4 The 'd' is silent, hillbilly.

[pdimens]

Hey there, sorry for the delayed response. Can you verify that there is a reference.fasta file in your working directory?

[santoshkumarrana]

Hi, I am running denovo assembly. I guess we don't need to provide reference.fasta in working directly. But instead, dDocent should be able to map the input reads and build reference.fasta itself. But its not working.

[pdimens]

The main dDocent executable does not automatically build a de novo assembly. You will need to use the included RefMap etc scripts to accomplish that.